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Opened 3 weeks ago
Closed 3 weeks ago
#19957 closed defect (fixed)
Boltz: 'str' object has no attribute 'chain_ids'
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Structure Prediction | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Linux-6.8.0-101-generic-x86_64-with-glibc2.35
ChimeraX Version: 1.11.1 (2026-01-23 05:51:34 UTC)
Description
Replace this text with list of actions that caused this problem to occur
Log:
Startup Messages
---
warning | GBM is not supported with the current configuration. Fallback to Vulkan rendering in Chromium.
UCSF ChimeraX version: 1.11.1 (2026-01-23)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open 3v33 fromDatabase pdb format mmcif
3v33 title:
Crystal structure of MCPIP1 conserved domain with zinc-finger motif [more
info...]
Chain information for 3v33 #1
---
Chain | Description | UniProt
A B | Ribonuclease ZC3H12A | ZC12A_HUMAN 112-334
3v33 mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
2778 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
> sequence chain #1/A#1/B
Alignment identifier is 1
> select clear
> select /A-B:134-296
2660 atoms, 2724 bonds, 1 pseudobond, 323 residues, 2 models selected
> ui tool show Boltz
> boltz predict protein
> GGGTPKAPNLEPPLPEEEKEGSDLRPVVIDGSNVAMSHGNKEVFSCRGILLAVNWFLERGHTDITVFVPSWRKEQPRPDVPITDQHILRELEKKKILVFTPSRRVGGKRVVCYDDRFIVKLAYESDGIVVSNDTYRDLQGERQEWKRFIEERLLMYSFVNDKFMPPDDPLGRHGPSLDNFLRKKPLTLEHRKQPCPYGRKCTYGIKCRFFHPERPSCPQRSVA
> ligandSmiles
> Cc1ccc(C(=O)Nc2ccc(S(=O)(=O)O)c3cc(S(=O)(=O)O)cc(S(=O)(=O)O)c23)cc1NC(=O)c1cccc(NC(=O)Nc2cccc(C(=O)Nc3cc(C(=O)Nc4ccc(S(=O)(=O)O)c5cc(S(=O)(=O)O)cc(S(=O)(=O)O)c45)ccc3C)c2)c1,[H]c1c([H])c(C(=O)N([H])c2c([H])c(C(=O)N([H])c3c([H])c([H])c(S(=O)(=O)[O-])c4c([H])c(S(=O)(=O)[O-])c([H])c(S(=O)(=O)[O-])c34)c([H])c([H])c2C([H])([H])[H])c([H])c(N([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])c2c([H])c(S(=O)(=O)[O-])c([H])c3c(S(=O)(=O)[O-])c([H])c([H])c(N([H])[H])c23)c1[H]
> name 3v33_sur_suramin_delta device gpu affinity each steering true samples
> 100
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/boltz/boltz_gui.py", line 587, in _predict
self._run_prediction(options = ' '.join(options))
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/boltz/boltz_gui.py", line 604, in _run_prediction
br = run(self.session, cmd)
^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/boltz/predict.py", line 85, in boltz_predict
br.start()
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/boltz/predict.py", line 531, in start
self._write_yaml_input_files()
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/boltz/predict.py", line 550, in _write_yaml_input_files
yaml = [(p.yaml_filename(self.name), p.yaml_input(msa_cache_dir)) for p in
self._predictions]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/boltz/predict.py", line 550, in <listcomp>
yaml = [(p.yaml_filename(self.name), p.yaml_input(msa_cache_dir)) for p in
self._predictions]
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/boltz/predict.py", line 352, in yaml_input
ligand_chain_id = self._predict_affinity.chain_ids[-1]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'str' object has no attribute 'chain_ids'
AttributeError: 'str' object has no attribute 'chain_ids'
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/boltz/predict.py", line 352, in yaml_input
ligand_chain_id = self._predict_affinity.chain_ids[-1]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
> boltz predict protein
> GGGTPKAPNLEPPLPEEEKEGSDLRPVVIDGSNVAMSHGNKEVFSCRGILLAVNWFLERGHTDITVFVPSWRKEQPRPDVPITDQHILRELEKKKILVFTPSRRVGGKRVVCYDDRFIVKLAYESDGIVVSNDTYRDLQGERQEWKRFIEERLLMYSFVNDKFMPPDDPLGRHGPSLDNFLRKKPLTLEHRKQPCPYGRKCTYGIKCRFFHPERPSCPQRSVA
> ligandSmiles
> Cc1ccc(C(=O)Nc2ccc(S(=O)(=O)O)c3cc(S(=O)(=O)O)cc(S(=O)(=O)O)c23)cc1NC(=O)c1cccc(NC(=O)Nc2cccc(C(=O)Nc3cc(C(=O)Nc4ccc(S(=O)(=O)O)c5cc(S(=O)(=O)O)cc(S(=O)(=O)O)c45)ccc3C)c2)c1,[H]c1c([H])c(C(=O)N([H])c2c([H])c(C(=O)N([H])c3c([H])c([H])c(S(=O)(=O)[O-])c4c([H])c(S(=O)(=O)[O-])c([H])c(S(=O)(=O)[O-])c34)c([H])c([H])c2C([H])([H])[H])c([H])c(N([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])c2c([H])c(S(=O)(=O)[O-])c([H])c3c(S(=O)(=O)[O-])c([H])c([H])c(N([H])[H])c23)c1[H]
> name 3v33_sur_suramin_delta device gpu affinity each steering true samples
> 100
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/boltz/boltz_gui.py", line 587, in _predict
self._run_prediction(options = ' '.join(options))
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/boltz/boltz_gui.py", line 604, in _run_prediction
br = run(self.session, cmd)
^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/boltz/predict.py", line 85, in boltz_predict
br.start()
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/boltz/predict.py", line 531, in start
self._write_yaml_input_files()
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/boltz/predict.py", line 550, in _write_yaml_input_files
yaml = [(p.yaml_filename(self.name), p.yaml_input(msa_cache_dir)) for p in
self._predictions]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/boltz/predict.py", line 550, in <listcomp>
yaml = [(p.yaml_filename(self.name), p.yaml_input(msa_cache_dir)) for p in
self._predictions]
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/boltz/predict.py", line 352, in yaml_input
ligand_chain_id = self._predict_affinity.chain_ids[-1]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'str' object has no attribute 'chain_ids'
AttributeError: 'str' object has no attribute 'chain_ids'
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/boltz/predict.py", line 352, in yaml_input
ligand_chain_id = self._predict_affinity.chain_ids[-1]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
> boltz predict protein
> GGGTPKAPNLEPPLPEEEKEGSDLRPVVIDGSNVAMSHGNKEVFSCRGILLAVNWFLERGHTDITVFVPSWRKEQPRPDVPITDQHILRELEKKKILVFTPSRRVGGKRVVCYDDRFIVKLAYESDGIVVSNDTYRDLQGERQEWKRFIEERLLMYSFVNDKFMPPDDPLGRHGPSLDNFLRKKPLTLEHRKQPCPYGRKCTYGIKCRFFHPERPSCPQRSVA
> ligandSmiles
> Cc1ccc(C(=O)Nc2ccc(S(=O)(=O)O)c3cc(S(=O)(=O)O)cc(S(=O)(=O)O)c23)cc1NC(=O)c1cccc(NC(=O)Nc2cccc(C(=O)Nc3cc(C(=O)Nc4ccc(S(=O)(=O)O)c5cc(S(=O)(=O)O)cc(S(=O)(=O)O)c45)ccc3C)c2)c1,[H]c1c([H])c(C(=O)N([H])c2c([H])c(C(=O)N([H])c3c([H])c([H])c(S(=O)(=O)[O-])c4c([H])c(S(=O)(=O)[O-])c([H])c(S(=O)(=O)[O-])c34)c([H])c([H])c2C([H])([H])[H])c([H])c(N([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])c2c([H])c(S(=O)(=O)[O-])c([H])c3c(S(=O)(=O)[O-])c([H])c([H])c(N([H])[H])c23)c1[H]
> name 3v33_sur_suramin_delta device gpu affinity each steering true samples
> 100
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/boltz/boltz_gui.py", line 587, in _predict
self._run_prediction(options = ' '.join(options))
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/boltz/boltz_gui.py", line 604, in _run_prediction
br = run(self.session, cmd)
^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/boltz/predict.py", line 85, in boltz_predict
br.start()
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/boltz/predict.py", line 531, in start
self._write_yaml_input_files()
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/boltz/predict.py", line 550, in _write_yaml_input_files
yaml = [(p.yaml_filename(self.name), p.yaml_input(msa_cache_dir)) for p in
self._predictions]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/boltz/predict.py", line 550, in <listcomp>
yaml = [(p.yaml_filename(self.name), p.yaml_input(msa_cache_dir)) for p in
self._predictions]
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/boltz/predict.py", line 352, in yaml_input
ligand_chain_id = self._predict_affinity.chain_ids[-1]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'str' object has no attribute 'chain_ids'
AttributeError: 'str' object has no attribute 'chain_ids'
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/boltz/predict.py", line 352, in yaml_input
ligand_chain_id = self._predict_affinity.chain_ids[-1]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 555.42.06
OpenGL renderer: NVIDIA GeForce RTX 3090/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.11.13
Locale: en_US.UTF-8
Qt version: PyQt6 6.9.1, Qt 6.9.0
Qt runtime version: 6.9.2
Qt platform: xcb
XDG_SESSION_TYPE=x11
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:1
Manufacturer: MouseComputer
Model: Z690-S01
OS: Ubuntu 22.04
Architecture: 64bit ELF
Virtual Machine: none
CPU: 24 12th Gen Intel(R) Core(TM) i9-12900K
Cache Size: 30720 KB
Memory:
total used free shared buff/cache available
Mem: 62Gi 3.9Gi 13Gi 138Mi 44Gi 58Gi
Swap: 2.0Gi 0B 2.0Gi
Graphics:
01:00.0 VGA compatible controller [0300]: NVIDIA Corporation GA102 [GeForce RTX 3090] [10de:2204] (rev a1)
Subsystem: ZOTAC International (MCO) Ltd. GA102 [GeForce RTX 3090] [19da:1613]
Kernel driver in use: nvidia
Installed Packages:
aiohappyeyeballs: 2.6.1
aiohttp: 3.13.1
aiosignal: 1.4.0
alabaster: 1.0.0
annotated-types: 0.7.0
anyio: 4.12.1
appdirs: 1.4.4
asttokens: 3.0.1
attrs: 25.4.0
babel: 2.17.0
beautifulsoup4: 4.13.5
blockdiag: 3.0.0
blosc2: 3.12.2
build: 1.3.0
certifi: 2026.1.4
cftime: 1.6.5
charset-normalizer: 3.4.4
ChimeraX-AddCharge: 1.5.20
ChimeraX-AddH: 2.2.8
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 3.1.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Animations: 1.0
ChimeraX-Aniso: 1.3.2
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.61.4
ChimeraX-AtomicLibrary: 14.2.1
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.1
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.6.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3.0
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.11.1
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.4
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5.3
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.4
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.7.3
ChimeraX-Label: 1.2
ChimeraX-LinuxSupport: 1.0.1
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.2
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.2.2
ChimeraX-MCopy: 1.0
ChimeraX-MCPServer: 0.1.0
ChimeraX-MDcrds: 2.17.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-Minimize: 1.3.2
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.22
ChimeraX-ModelPanel: 1.6
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0.1
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.15.2
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.12
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.5
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.4
ChimeraX-ProfileGrids: 1.4.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.5
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.3
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.2
ChimeraX-Scenes: 0.3.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.10
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.3
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.49.1
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDock: 1.5.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.5
ChimeraX-Zone: 1.0.1
click: 8.3.1
colorama: 0.4.6
comm: 0.2.3
contourpy: 1.3.3
coverage: 7.13.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.1.4
debugpy: 1.8.19
decorator: 5.2.1
distro: 1.9.0
docutils: 0.21.2
executing: 2.2.1
filelock: 3.19.1
fonttools: 4.61.1
frozenlist: 1.8.0
funcparserlib: 2.0.0a0
glfw: 2.10.0
grako: 3.16.5
h11: 0.16.0
h5py: 3.15.1
html2text: 2025.4.15
httpcore: 1.0.9
httpx: 0.28.1
httpx-sse: 0.4.3
idna: 3.11
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.3.0
ipykernel: 6.30.1
ipython: 9.5.0
ipython_pygments_lexers: 1.1.1
ipywidgets: 8.1.8
jedi: 0.19.2
Jinja2: 3.1.6
jsonschema: 4.26.0
jsonschema-specifications: 2025.9.1
jupyter_client: 8.6.3
jupyter_core: 5.9.1
jupyterlab_widgets: 3.0.16
kiwisolver: 1.4.9
line_profiler: 5.0.0
lxml: 6.0.2
lz4: 4.3.2
Markdown: 3.8.2
MarkupSafe: 3.0.3
matplotlib: 3.10.7
matplotlib-inline: 0.2.1
mcp: 1.18.0
msgpack: 1.1.1
multidict: 6.7.0
ndindex: 1.10.1
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.14.1
numpy: 1.26.4
nvidia-nvjitlink-cu12: 12.9.86
OpenMM: 8.2.0
OpenMM-CUDA-12: 8.2.0
openvr: 1.26.701
packaging: 25.0
ParmEd: 4.2.2
parso: 0.8.5
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 11.3.0
pip: 25.2
pkginfo: 1.12.1.2
platformdirs: 4.5.1
pluggy: 1.6.0
prompt_toolkit: 3.0.52
propcache: 0.4.1
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pybind11: 3.0.1
pycollada: 0.8
pydantic: 2.12.5
pydantic-settings: 2.12.0
pydantic_core: 2.41.5
pydicom: 2.4.4
Pygments: 2.18.0
pynmrstar: 3.3.6
pynrrd: 1.0.0
PyOpenGL: 3.1.10
PyOpenGL-accelerate: 3.1.10
pyopenxr: 1.1.4501
pyparsing: 3.3.2
pyproject_hooks: 1.2.0
PyQt6: 6.9.1
PyQt6-Qt6: 6.9.2
PyQt6-WebEngine: 6.9.0
PyQt6-WebEngine-Qt6: 6.9.2
PyQt6_sip: 13.10.2
pytest: 9.0.2
pytest-cov: 7.0.0
python-dateutil: 2.9.0.post0
python-dotenv: 1.2.1
python-multipart: 0.0.21
pyzmq: 27.1.0
qtconsole: 5.7.0
QtPy: 2.4.3
qtshim: 1.2
RandomWords: 0.4.0
referencing: 0.37.0
requests: 2.32.5
roman-numerals: 4.1.0
roman-numerals-py: 4.1.0
rpds-py: 0.30.0
scipy: 1.14.0
setuptools: 80.9.0
sfftk-rw: 0.8.1
six: 1.17.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.8.3
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.2.0
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
sse-starlette: 3.2.0
stack-data: 0.6.3
starlette: 0.52.1
superqt: 0.7.6
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.5
tornado: 6.5.4
traitlets: 5.14.3
typing-inspection: 0.4.2
typing_extensions: 4.15.0
urllib3: 2.6.3
uvicorn: 0.40.0
wcwidth: 0.3.2
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.15
yarl: 1.22.0
Change History (2)
comment:1 by , 3 weeks ago
| Component: | Unassigned → Structure Prediction |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Boltz: 'str' object has no attribute 'chain_ids' |
comment:2 by , 3 weeks ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
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User specified "affinity each" in boltz predict command but did not specify forEachSmilesLigand option. This can be done with the Boltz GUI if you add "for each ligand smiles" then later delete that molecular component. I added error reporting in the command to explain the problem instead of reporting a traceback.